Herbert M Sauro
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Explore the profile of Herbert M Sauro including associated specialties, affiliations and a list of published articles.
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Recent Articles
11.
Kochen M, Hellerstein J, Sauro H
Interface Focus
. 2024 Feb;
14(1):20230045.
PMID: 38344405
Cellular signal transduction takes place through a network of phosphorylation cycles. These pathways take the form of a multi-layered cascade of cycles. This work focuses on the sensitivity of single,...
12.
Andrews S, Wiley H, Sauro H
Bioessays
. 2024 Jan;
46(3):e2300188.
PMID: 38247191
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we...
13.
Ma S, Fan L, Konanki S, Liu E, Gennari J, Smith L, et al.
Bioinformatics
. 2023 Dec;
39(12).
PMID: 38096590
Motivation: Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface. However, as with the...
14.
Shin W, Gennari J, Hellerstein J, Sauro H
Bioinformatics
. 2023 Oct;
39(11).
PMID: 37882737
Motivation: Annotations of biochemical models provide details of chemical species, documentation of chemical reactions, and other essential information. Unfortunately, the vast majority of biochemical models have few, if any, annotations,...
15.
Andrews S, Wiley H, Sauro H
ArXiv
. 2023 Oct;
PMID: 37873010
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we...
16.
Sego T, Sluka J, Sauro H, Glazier J
PLoS Comput Biol
. 2023 Oct;
19(10):e1010768.
PMID: 37871133
Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based...
17.
Kochen M, Hellerstein J, Sauro H
bioRxiv
. 2023 Oct;
PMID: 37781602
Signal transduction from a cell's surface to cytoplasmic and nuclear targets takes place through a complex network of interconnected pathways. Phosphorylation cycles are common components of many pathways and may...
18.
Jakubowski H, Agnew H, Jardine B, Sauro H
ArXiv
. 2023 Sep;
PMID: 37731655
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their...
19.
Jardine B, Smith L, Sauro H
ArXiv
. 2023 Sep;
PMID: 37731653
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web application that...
20.
Xu J, Geng G, Nguyen N, Perena-Cortes C, Samuels C, Sauro H
ArXiv
. 2023 Aug;
PMID: 37645048
SBcoyote is an open-source cross-platform biochemical reaction viewer and editor released under the liberal MIT license. It is written in Python and uses wxPython to implement the GUI and the...